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Al Amaz S, Shahid MAH, Jha R, Mishra B. Prehatch thermal manipulation of embryos and posthatch baicalein supplementation increased liver metabolism, and muscle proliferation in broiler chickens. Poult Sci 2024; 103:104155. [PMID: 39216265 PMCID: PMC11402044 DOI: 10.1016/j.psj.2024.104155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/28/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
The exposure of broiler chickens to high ambient temperatures causes heat stress (HS), negatively affecting their health and production performance. To mitigate heat stress in broilers, various strategies, including dietary, managerial, and genetic interventions, have been extensively tested with varying degrees of efficacy. For sustainable broiler production, it is imperative to develop an innovative approach that effectively mitigates the adverse effects of HS. Our previous studies have provided valuable insights into the effects of prehatch embryonic thermal manipulation (TM) and posthatch baicalein supplementation on embryonic thermotolerance, metabolism, and posthatch growth performance. This follow-up study investigated the effect of these interventions on gluconeogenesis and lipid metabolism in the liver, as well as muscle proliferation and regeneration capacity in heat-stressed broiler chickens. A total of six-hundred fertile Cobb 500 eggs were incubated for 21 d. After candling, 238 eggs were subjected to TM at 38.5°C with 55% relative humidity (RH) from embryonic day (ED) 12 to 18. These eggs were transferred to the hatcher and kept at a standard temperature (37.5°C) from ED 19 to 21, while 236 eggs were incubated at a controlled temperature (37.5°C) till hatch. After hatching, 180 day-old chicks from both groups were raised in 36 pens treatment (n = 10 birds/pen, 6 replicates per treatment). The treatments were: 1) Control, 2) TM, 3) Control heat stress (CHS), 4) Thermal manipulation heat stress (TMHS), 5) Control heat stress supplement (CHSS), and 6) Thermal manipulation heat stress supplement (TMHSS). Baicalein was added to the treatment group diets starting from d 1. All birds were raised under the standard environment for 21 d, followed by chronic heat stress from d 22 to 35 (32-33 ⁰C for 8 h) in the CHS, TMHS, CHSS, and TMHSS groups. A thermoneutral (22-24⁰C) environment was maintained in the Control and TM groups. RH was constant (50 ± 5%) throughout the trial. In the liver, TM significantly increased (P < 0.05) IGF2 expression. Baicalein supplementation significantly increased (P < 0.05) HSF3, HSP70, SOD1, SOD2, TXN, PRARα, and GHR expression. Moreover, the combination of TM and baicalein supplementation significantly increased (P < 0.05) the expression of HSPH1, HSPB1, HSP90, LPL, and GHR. In the muscle, TM significantly increased (P < 0.05) HSF3 and Myf5 gene expression. TM and baicalein supplementation significantly increased (P < 0.05) the expression of MyoG and significantly (P < 0.05) decreased mTOR and PAX7. In conclusion, the prehatch TM of embryos and posthatch baicalein supplementation mitigated the deleterious effects of HS on broiler chickens by upregulating genes related to liver gluconeogenesis, lipid metabolism, and muscle proliferation.
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Affiliation(s)
- Sadid Al Amaz
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Manoa, Honolulu, HI 96822
| | - Md Ahosanul Haque Shahid
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Manoa, Honolulu, HI 96822
| | - Rajesh Jha
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Manoa, Honolulu, HI 96822
| | - Birendra Mishra
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Manoa, Honolulu, HI 96822.
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Liu Y, Sun D, Xu C, Liu X, Tang M, Ying S. In-depth transcriptome profiling of Cherry Valley duck lungs exposed to chronic heat stress. Front Vet Sci 2024; 11:1417244. [PMID: 39104549 PMCID: PMC11298465 DOI: 10.3389/fvets.2024.1417244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024] Open
Abstract
Amidst rising global temperatures, chronic heat stress (CHS) is increasingly problematic for the poultry industry. While mammalian CHS responses are well-studied, avian-specific research is lacking. This study uses in-depth transcriptome sequencing to evaluate the pulmonary response of Cherry Valley ducks to CHS at ambient temperatures of 20°C and a heat-stressed 29°C. We detailed the CHS-induced gene expression changes, encompassing mRNAs, lncRNAs, and miRNAs. Through protein-protein interaction network analysis, we identified central genes involved in the heat stress response-TLR7, IGF1, MAP3K1, CIITA, LCP2, PRKCB, and PLCB2. Subsequent functional enrichment analysis of the differentially expressed genes and RNA targets revealed significant engagement in immune responses and regulatory processes. KEGG pathway analysis underscored crucial immune pathways, specifically those related to intestinal IgA production and Toll-like receptor signaling, as well as Salmonella infection and calcium signaling pathways. Importantly, we determined six miRNAs-miR-146, miR-217, miR-29a-3p, miR-10926, miR-146b-5p, and miR-17-1-3p-as potential key regulators within the ceRNA network. These findings enhance our comprehension of the physiological adaptation of ducks to CHS and may provide a foundation for developing strategies to improve duck production under thermal stress.
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Affiliation(s)
- Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Dongyue Sun
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Congcong Xu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xiaoyong Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shijia Ying
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Lu T, Abdalla Gibril BA, Xu J, Xiong X. Unraveling the Genetic Foundations of Broiler Meat Quality: Advancements in Research and Their Impact. Genes (Basel) 2024; 15:746. [PMID: 38927682 PMCID: PMC11202585 DOI: 10.3390/genes15060746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
As societal progress elevates living standards, the focus on meat consumption has shifted from quantity to quality. In broiler production, optimizing meat quality has become paramount, prompting efforts to refine various meat attributes. Recent advancements in sequencing technologies have revealed the genome's complexity, surpassing previous conceptions. Through experimentation, numerous genetic elements have been linked to crucial meat quality traits in broiler chickens. This review synthesizes the current understanding of genetic determinants associated with meat quality attributes in broilers. Researchers have unveiled the pivotal insights detailed herein by employing diverse genomic methodologies such as QTL-based investigations, candidate gene studies, single-nucleotide polymorphism screening, genome-wide association studies, and RNA sequencing. These studies have identified numerous genes involved in broiler meat quality traits, including meat lightness (COL1A2 and ACAA2), meat yellowness (BCMO1 and GDPD5), fiber diameter (myostatin and LncIRS1), meat pH (PRDX4), tenderness (CAPN1), and intramuscular fat content (miR-24-3p and ANXA6). Consequently, a comprehensive exploration of these genetic elements is imperative to devise novel molecular markers and potential targets, promising to revolutionize strategies for enhancing broiler meat quality.
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Affiliation(s)
| | | | | | - Xinwei Xiong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang 330032, China
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Yu S, Wang G, Shen X, Chen J, Liao J, Yang Y, Aikebai G. Comprehensive analysis of changes in expression of lncRNA, microRNA and mRNA in liver tissues of chickens with high or low abdominal fat deposition. Br Poult Sci 2024; 65:250-258. [PMID: 38808584 DOI: 10.1080/00071668.2024.2319779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/07/2023] [Indexed: 05/30/2024]
Abstract
1. The liver of chickens is a dominant lipid biosynthetic tissue and plays a vital role in fat deposition, particularly in the abdomen. To determine the molecular mechanisms involved in its lipid metabolism, the livers of chickens with high (H) or low (L) abdominal fat content were sampled and sequencing on long non-coding RNA (lncRNA), messenger RNA (mRNA) and small RNA (microRNA) was performed.2. In total, 351 expressed protein-coding genes for long non-coding RNA (DEL; 201 upregulated and 150 downregulated), 400 differentially expressed genes (DEG; 223 upregulated and 177 downregulated) and 10 differentially expressed miRNA (DEM; four upregulated and six downregulated) were identified between the two groups. Multiple potential signalling pathways related to lipogenesis and lipid metabolism were identified via pathway enrichment analysis. In addition, 173 lncRNA - miRNA - mRNA interaction regulatory networks were identified, including 30 lncRNA, 27 mRNA and seven miRNA.3. These networks may help regulate lipid metabolism and fat deposition. Five promising candidate genes and two lncRNA may play important roles in the regulation of adipogenesis and lipid metabolism in chickens.
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Affiliation(s)
- S Yu
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - G Wang
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - X Shen
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - J Chen
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - J Liao
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - Y Yang
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - G Aikebai
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
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Amaz SA, Shahid MAH, Chaudhary A, Jha R, Mishra B. Embryonic thermal manipulation reduces hatch time, increases hatchability, thermotolerance, and liver metabolism in broiler embryos. Poult Sci 2024; 103:103527. [PMID: 38412748 PMCID: PMC10907853 DOI: 10.1016/j.psj.2024.103527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/29/2024] Open
Abstract
The broilers' health and growth performance are affected by egg quality, incubation conditions, and posthatch management. Broilers are more susceptible to heat stress because they have poor thermoregulatory capacity. So, it is crucial to develop a strategy to make chicks thermotolerant and cope with heat stress in post-hatch life. This study investigated the effects of embryonic thermal manipulation (TM) on different hatching parameters (hatch time, hatchability, and hatch weight), brain thermotolerance, and liver metabolism. Six hundred fertile Cobb 500 eggs were incubated for 21 d. After candling on embryonic day (ED) 10, 238 eggs were thermally manipulated at 38.5°C with 55% relative humidity (RH) from ED 12 to 18, then transferred to the hatcher (ED 19-21, standard temperature, 37.5°C) and 236 eggs were incubated at a standard temperature (37.5°C) till hatch. The samples were collected from the Control and TM groups on ED 15 and 18 of the embryonic periods. Hatchability was significantly higher (P < 0.05) in the TM group (94.50%) than in the control group (91.0%). Hatch weight did not differ significantly between the TM group (50.54 g) and the Control group (50.39 g). Most importantly, hatch time was significantly lower (P < 0.05) in the TM group than in the Control. In the D15 embryo brain, the mRNA expression of TRPV1,TRPV2, TRPV3, and the epigenetic marker H3K27 were significantly lower (P < 0.05) in the TM group compared to the Control group. However, in the D18 brain, the expression of TRPV1, TRPV2, and CRHR1 was significantly higher (P < 0.05) in the TM group than in the Control group. In the liver, the mRNA expression of SLC6A14 was significantly lower (P < 0.05) in the D15 TM group than in the D15 Control group. Conversely, the DIO3 mRNA expression was significantly higher (P < 0.05) in the D15 TM group than in the D15 Control group. The expression of GPX3, FOXO1, IGF2, and GHR in the liver was significantly higher in the D18 TM group compared to the D18 Control group (P < 0.05). In conclusion, increased expression of the aforementioned markers during the later embryonic period has been linked to reduced hatch time by increasing liver metabolism and thermotolerance capacity in the brain.
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Affiliation(s)
- Sadid Al Amaz
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, Hawaii, 96822
| | - Md Ahosanul Haque Shahid
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, Hawaii, 96822
| | - Ajay Chaudhary
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, Hawaii, 96822
| | - Rajesh Jha
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, Hawaii, 96822
| | - Birendra Mishra
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, Hawaii, 96822.
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Aboelhassan DM, Darwish HR, Mansour H, Abozaid H, Ghaly IS, Radwan HA, Hassan ER, Farag IM. Polymorphisms and expressions of ADSL, MC4R and CAPN1 genes and their effects on economic traits in Egyptian chicken breeds. Mol Biol Rep 2023; 51:4. [PMID: 38071695 PMCID: PMC10710965 DOI: 10.1007/s11033-023-08999-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/11/2023] [Indexed: 12/18/2023]
Abstract
In recent years, strategic plans for poultry production have emphasized quantitative traits, particularly body weight and carcass traits (meat yield), in response to overpopulation challenges. Candidate genes such as adenylosuccinate lyase (ADSL), melanocortin-4-receptor (MC4R), and calpain 1 (CAPN1) have played vital roles in this context due to their associations with muscle growth and body composition. This study aims to investigate the influence of polymorphisms and gene expressions of the aforementioned genes on body weight (BW), growth rate (GR), breast weight (BrW), and thigh weight (TW) across four distinct chicken breeds: Fayoumi, Matrouh, Mamourah, and Leghorn. The use of PCR-SSCP analysis revealed genetic polymorphisms through the identification of various patterns (genotypes) within the three examined genes. The ADSL, MC4R, and CAPN1 genes exhibited five, three, and two different genotypes, respectively. These polymorphisms displayed promising connections with enhancing economically significant production traits, particularly BW, BrW and TW. Furthermore, gene expression analyses were conducted on breast and thigh tissues obtained from the chicken breeds at 60 days of age, where ADSL and MC4R exhibited a noteworthy up-regulation in Fayoumi and Matrouh breeds, and down-regulation in Mamourah and Leghorn. In contrast, CAPN1 expression decreased across most breeds with a slight increase noted in Fayoumi breed. In conclusion, this investigation underscores the substantial impact of ADSL, MC4R, and CAPN1 genes on economically important production traits within Egyptian domestic chicken breeds. Consequently, these genes emerge as significant molecular markers, holding potential utility in avian selection and breeding programs aimed at enhancing productive performance.
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Affiliation(s)
- Dalia M Aboelhassan
- Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33st El Bohouth, Dokki, Giza, 12622, Egypt.
| | - Hassan R Darwish
- Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33st El Bohouth, Dokki, Giza, 12622, Egypt
| | - Hayam Mansour
- Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33st El Bohouth, Dokki, Giza, 12622, Egypt
| | - Hesham Abozaid
- Department of Animal Production, Agricultural and Biology Institute, National Research Centre, Giza, 12622, Egypt
| | - Inas S Ghaly
- Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33st El Bohouth, Dokki, Giza, 12622, Egypt
| | - Hasnaa A Radwan
- Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33st El Bohouth, Dokki, Giza, 12622, Egypt
| | - Eman R Hassan
- Department of Poultry Disease, Veterinary Research Institute, National Research Centre, Giza, 12622, Egypt
| | - Ibrahim M Farag
- Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33st El Bohouth, Dokki, Giza, 12622, Egypt
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7
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Mariandayani HN, Darwati S, Khaerunnisa I, Prasasty VD. Growth performance of Indonesian three-breed cross chicken associated with growth hormone and insulin-like growth factor 2 genes. Vet World 2023; 16:2471-2478. [PMID: 38328357 PMCID: PMC10844795 DOI: 10.14202/vetworld.2023.2471-2478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/15/2023] [Indexed: 02/09/2024] Open
Abstract
Background and Aim Poultry, such as chickens, is an important source of animal protein, producing eggs and meat. Local chickens are able to adapt to the hot weather and become more resistant to disease. However, it has relatively slow growth and low egg production. These problems can be overcome through holding selection and crossing. Local chicken productivity is slow and low based on chicken growth. There is a need to examine the factors that influence growth and productivity. Therefore, this study aimed to evaluate crossbreed chicken growth performance, including body weight (BW), BW gain, feed intake, and feed conversion. Materials and Methods DNA was extracted from 40 chickens with the growth hormone (GH) gene and 40 chickens with the insulin-like growth factor 2 (IGF2) gene, followed by a polymerase chain reaction. Genotyping was performed using restriction fragment length polymorphism analysis. In animal selection and phenotypic data collection, 80 chickens from Sentul, Kampung, and Kedu were used to produce the second-generation three-crossbreed chickens (F2) using the GH gene. Results Growth hormone is a very relevant gene in chicken performance traits. Growth hormone and IGF2 genes regulate chicken production. This study presents the second-generation growth features of three-crossbreed chickens derived from Sentul, Kampung, and Kedu, all of which are native to Indonesia (F2). A statistically significant (p = 0.05) improvement in BW, weight gain, feed intake, and feed conversion over a 12-week period was observed when the animals were allowed free access to regular feed. Analysis of variance results indicated a significant (p = 0.0001) interaction between the 12-week period and GH and IGF2 gene sensitivities of different chicken breeds. Conclusion Crossbreed chicken growth performance increased within 12 weeks. This study highlighted the need to improve the productivity and breeding of domestic crossbred chickens to contribute to the Indonesian conservation and genetic diversity program.
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Affiliation(s)
| | - Sri Darwati
- Department of Animal Production and Technology, Faculty of Animal Husbandry, Bogor Agricultural University, Bogor, West Java 16680, Indonesia
| | - Isyana Khaerunnisa
- Research Center for Applied Zoology, National Research and Innovation Agency, Bogor, West Java 16912, Indonesia
| | - Vivitri Dewi Prasasty
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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Yang K, Zhang J, Zhao Y, Shao Y, Zhai M, Liu H, Zhang L. Whole Genome Resequencing Revealed the Genetic Relationship and Selected Regions among Baicheng-You, Beijing-You, and European-Origin Broilers. BIOLOGY 2023; 12:1397. [PMID: 37997996 PMCID: PMC10669838 DOI: 10.3390/biology12111397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens.
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Affiliation(s)
- Kai Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Jian Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Yuelei Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Yonggang Shao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Manjun Zhai
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
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Moreira LR, Smith BT. Convergent genomic signatures of local adaptation across a continental-scale environmental gradient. SCIENCE ADVANCES 2023; 9:eadd0560. [PMID: 37205757 PMCID: PMC10198635 DOI: 10.1126/sciadv.add0560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 04/17/2023] [Indexed: 05/21/2023]
Abstract
Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in adaptive evolution, in particular the extent to which similar genetic mechanisms drive adaptation to common selective forces. Here, we investigated the genomics of local adaptation in two nonsister woodpeckers that are codistributed across an entire continent and exhibit remarkably convergent patterns of geographic variation. We sequenced the genomes of 140 individuals of Downy (Dryobates pubescens) and Hairy (Dryobates villosus) woodpeckers and used a suite of genomic approaches to identify loci under selection. We showed evidence that convergent genes have been targeted by selection in response to shared environmental pressures, such as temperature and precipitation. Among candidates, we found multiple genes putatively linked to key phenotypic adaptations to climate, including differences in body size (e.g., IGFPB) and plumage (e.g., MREG). These results are consistent with genetic constraints limiting the pathways of adaptation to broad climatic gradients, even after genetic backgrounds diverge.
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Affiliation(s)
- Lucas R. Moreira
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
- Department of Ornithology, American Museum of Natural History, New York City, NY, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York City, NY, USA
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Beneficial impact of dietary methyl methionine sulfonium chloride and/or L-carnitine supplementation on growth performance, feed efficiency, and serum biochemical parameters in broiler chicken: role of IGF-1 and MSTN genes. Trop Anim Health Prod 2022; 54:98. [PMID: 35141787 DOI: 10.1007/s11250-022-03065-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
The purpose of this study was to examine the effect of dietary supplementation with methyl methionine sulfonium chloride (MMSC), and L-carnitine (L-CAR) alone or in combination on the growth performance of broilers through their impact on the expression of IGF-1 and MSTN genes associated with growth in broilers. One-day-old female Ross 308 broiler chicks were allocated into four groups, each of which received a broiler starter diet and water daily ad libitum. The control group (group 1) was given drinking water without any additives. Group 2 received 0.25 g L-carnitine per liter of drinking water, group 3 received 0.25 g MMSC per liter of drinking water, and group 4 received 0.25 g of both L-carnitine and MMSC per liter of drinking water. Birds were given a starter diet to 21 days after which they received a broiler grower diet to 35 days when the experiment ended. There were five replicate groups of 12 birds per treatment. Body weights and feed intake were recorded weekly. Compared to the control group of birds, supplementation with MMSC either alone or in combination with L-carnitine resulted in an increase in growth rate or feed utilization efficiency; L-carnitine by itself had no effect. MMSC supplementation, again either alone or in combination with L-carnitine, increased jejunal and ileal villi height, increased serum total proteins and globulins, downregulated myostatin (MSTN) mRNA, and upregulated insulin growth factor-1 (IGF-1) mRNA expression. Supplementation with L-carnitine alone showed none of these effects. We conclude that MMSC supplementation improved growth performance through the upregulation of IGF-1 mRNA expression and downregulation of MSTN mRNA expression.
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11
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Ogunpaimo OJ, Ojoawo HT, Wheto MY, Adebambo AO, Adebambo OA. Association of insulin-like growth factor 1 (IGF1) gene polymorphism with the reproductive performance of three dual-purpose chicken breeds. Transl Anim Sci 2021; 5:txab215. [PMID: 34988376 PMCID: PMC8706822 DOI: 10.1093/tas/txab215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/11/2021] [Indexed: 11/14/2022] Open
Abstract
The study was designed to investigate the association of Insulin-like growth factor 1 (IGF1) gene polymorphism with the reproductive performance of FUNAAB-Alpha, Sasso, and Kuroiler dual-purpose chicken breeds. To achieve this, a total of 250 healthy hens were selected at 12 wk of age and were intensively managed in cages for 52 wk. Blood sample was taken from each chicken at the 34th week and genomic DNA was extracted using Qiagentm DNA extraction kit, PCR was used to amplify the DNA fragments, and the PCR products were electrophoresed. Amplicons obtained were digested with restriction enzyme hinf1, and were further electrophoresed on 1.5% agarose gel. Data obtained were analyzed using the General linear model of SAS (2002) version 9.0 to determine the effect of IGF1 gene polymorphism and the distribution of alleles within the breeds. Results show polymorphism of the IGF1 gene and the restriction analysis indicated two alleles; A 58% and C 42% with the identification of genotypes AA, AC, and CC, and genotypic frequency of 22%, 43%, and 35%, respectively. Significant associations were observed between the polymorphism of the IGF1 gene, age of the bird at first lay, and weight of the hen at first lay. Chickens with haplotype CC came earlier into lay compared to those with the other two haplotypes (AA and AC). Therefore, the study suggests that haplotype CC could be used as a genetic marker to select for an improved laying performance in chickens.
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Affiliation(s)
- Olaiwola J Ogunpaimo
- Directorate of University Farms, Federal University of Agriculture, Abeokuta, Ogun State, PMB 2240, Nigeria
| | - Henry T Ojoawo
- Center of Excellence in Agricultural Development and Sustainable Environment, Federal University of Agriculture, Abeokuta, Ogun State, PMB 2240, Nigeria
| | - Mathew Y Wheto
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, PMB 2240, Nigeria
| | - Ayotunde O Adebambo
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, PMB 2240, Nigeria
| | - Olufunmilayo A Adebambo
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, PMB 2240, Nigeria
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Prakash A, Saxena VK, Kumar R, Tomar S, Singh MK, Singh G. Differential gene expression in liver of colored broiler chicken divergently selected for residual feed intake. Trop Anim Health Prod 2021; 53:403. [PMID: 34268607 DOI: 10.1007/s11250-021-02844-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Feed constitutes about 60-70% of the total cost of poultry production. So maximizing the feed efficiency will reduce production cost. The rapid growth in the juvenile period is essential to achieve higher body weight. Therefore, identifying the genes and pathways involved in rapid growth at an early age with a lesser requirement of feed is of utmost importance to further economize the broiler production. The efficiency of feed utilization was measured using RFI (residual feed intake). The present study aimed to estimate the RFI (0-5 week) in a population of indigenously developed colored broiler sire line chicken as well as identifying the differentially expressed genes influencing RFI in high and low RFI groups. The liver samples of high and low RFI broiler chicken aged 35 days were used for microarray analysis. A total of 2798 differentially expressed genes (DEGs) were identified, out of which 913 genes were downregulated and 1885 were upregulated. The fold change varied from - 475.17 to 552.94. A subset of genes was confirmed by qRT-PCR, and outcomes were matched well with microarray data. In the functional annotation study of DEGs, the highest significant GO (Gene Ontology) terms in the biological process included protein transport, protein localization, regulation of apoptosis, and mitochondrial transport. Gene network analysis of these DEGs plays an important role to understand the interaction among genes. Study of the important genes which were differentially expressed and the related molecular pathways in this population may hold the potential for future breeding strategies for augmenting feed efficiency.
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Affiliation(s)
- A Prakash
- College of Veterinary Science, GADVASU, Rampura Phul, Bathinda, Punjab, India.
| | - V K Saxena
- Division of Avian Genetics and Breeding, Central Avian Research Institute - Indian Council of Agricultural Research, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Ravi Kumar
- Department of Animal Biotechnology, National Institute of Animal Biotechnology, Hyderabad, 500075, Telangana, India
| | - S Tomar
- Division of Avian Genetics and Breeding, Central Avian Research Institute - Indian Council of Agricultural Research, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - M K Singh
- COVS, DUVASU, Mathura, Uttar Pradesh, India
| | - Gagandeep Singh
- College of Veterinary Science, GADVASU, Rampura Phul, Bathinda, Punjab, India
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13
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Wang WJ, Guo YQ, Xie KJ, Li YD, Li ZW, Wang N, Xiao F, Guo HS, Li H, Wang SZ. A functional variant in the promoter region of IGF1 gene is associated with chicken abdominal fat deposition. Domest Anim Endocrinol 2021; 75:106584. [PMID: 33276215 DOI: 10.1016/j.domaniend.2020.106584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/26/2020] [Accepted: 11/03/2020] [Indexed: 12/29/2022]
Abstract
Insulin-like growth factor 1 (IGF1) plays an important role in the regulation of cell growth, proliferation, differentiation, and apoptosis. Previously several studies revealed that genotypes of chicken IGF1 c.-366A > C were significantly associated with abdominal fat weight and body weight in chickens. But the underlying mechanism is still unknown. To investigate the mechanism underlying the association, herein, we performed IGF1 gene mRNA expression profiling, a dual-luciferase reporter assay and electrophoretic mobility shift assay (EMSA). Quantitative real-time PCR results showed that IGF1 gene was widely expressed in 14 tissues. The mRNA expression levels of IGF1 gene in both abdominal fat and jejunum were significantly higher in fat broilers than in lean broilers. However, the opposite results were observed in the pancreas. The reporter gene assay showed that the promoter luciferase activity of allele A was significantly higher than that of allele C (P < 0.05). In addition, the luciferase activity of allele A promoted by the transcription factor AP1 and OCT1 was higher than that of allele C (P < 0.05). Electrophoretic mobility shift assay result showed that allele A binding to the transcription factor AP1 and OCT1 was stronger than that of allele C. All in all, our data indicated that the IGF1 gene c.-366A > C is a functional SNP responsible for chicken adipose deposition.
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Affiliation(s)
- W J Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Y Q Guo
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - K J Xie
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Y D Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Z W Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - N Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - F Xiao
- Fujian Sunnzer Biotechnology Development Co, Ltd, Guangze, Fujian Province 354100, China
| | - H S Guo
- Fujian Sunnzer Biotechnology Development Co, Ltd, Guangze, Fujian Province 354100, China
| | - H Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - S Z Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China.
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14
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Sinpru P, Bunnom R, Poompramun C, Kaewsatuan P, Sornsan S, Kubota S, Molee W, Molee A. Association of growth hormone and insulin-like growth factor I genotype with body weight, dominance of body weight, and mRNA expression in Korat slow-growing chickens. Anim Biosci 2021; 34:1886-1894. [PMID: 33705631 PMCID: PMC8563241 DOI: 10.5713/ab.20.0729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/27/2021] [Indexed: 12/02/2022] Open
Abstract
Objective Growth hormone (GH) and insulin-like growth factor I (IGF-I) play a critical role in animal growth rates. We aimed to investigate the effect of GH and IGF-I genotypes on body weight (BW), dominance, and gene expression in slow-growing chickens at different ages. Methods A total of 613 Korat chickens (KRs) were bred and divided into three groups by genotype – A1A1, A1A3, and A3A3 for GH and AA, AC, and CC for IGF-I. Chickens were weighed every two weeks, and liver and breast muscle tissues were collected at 10 weeks of age. Genetic parameters of KRs were estimated using ASReml software. The GH and IGF-I mRNA levels were measured by quantitative polymerase chain reaction. Significant differences between traits were analyzed using the generalized linear model. Results A significant effect of GH genotypes on BW was found at most ages, and the A1A1 genotype had the highest value of BW. Compared with the A3A3 genotype, the A1A1 and A1A3 genotypes showed a higher dominance effect at 0 and 2 weeks, and genotype A1A1 had the highest value of dominance at 8 weeks of age. A difference in GH mRNA levels between genotypes was detected in breast muscle at 6 weeks and in the liver tissue at 2 weeks. In the case of IGF-I gene, the AA genotype had the highest BW at the beginning of life. Significant differences in BW dominance were found at 2 weeks. However, IGF-I mRNA levels were not different among genotypes in both breast muscles and liver tissues. Conclusion Our results revealed that GH and IGF-I influence growth, but may not be involved in heterosis. GH can be used as a marker gene in selection programs for growth because the homozygous genotype (A1A1) had the highest BW at all ages. The IGF-I is not a useful marker gene for selection programs.
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Affiliation(s)
- Panpradub Sinpru
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Rujjira Bunnom
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Chotima Poompramun
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Pramin Kaewsatuan
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Sirangkun Sornsan
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Satoshi Kubota
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Wittawat Molee
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Amonrat Molee
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
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15
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Fouad AM, El-Senousey HK, Ruan D, Wang S, Xia W, Zheng C. Tryptophan in poultry nutrition: Impacts and mechanisms of action. J Anim Physiol Anim Nutr (Berl) 2021; 105:1146-1153. [PMID: 33655568 DOI: 10.1111/jpn.13515] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/23/2021] [Accepted: 02/08/2021] [Indexed: 01/09/2023]
Abstract
Many studies have shown that productivity, immune system, antioxidant status, and meat and egg quality can be optimized by dietary supplementation with amino acids that are not usually added to poultry diets. Understanding the effects of these amino acids may encourage feed manufacturers and poultry producers to include them as additives. One of these amino acids is tryptophan (Trp). The importance of Trp is directly related to its role in protein anabolism and indirectly related to its metabolites such as serotonin and melatonin. Thus, Trp could affect the secretion of hormones, development of immune organs, meat and egg production, and meat and egg quality in poultry raised under controlled or stressed conditions. Therefore, this review discusses the main roles of Trp in poultry production and its mode (s) of action in order to help poultry producers decide whether they need to add Trp to poultry diets. Further areas of research are also identified to address information gaps.
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Affiliation(s)
- Ahmed Mohamed Fouad
- Key Laboratory of Animal Nutrition and Feed Science (South China) of Ministry of Agriculture, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - HebatAllah Kasem El-Senousey
- Key Laboratory of Animal Nutrition and Feed Science (South China) of Ministry of Agriculture, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Dong Ruan
- Key Laboratory of Animal Nutrition and Feed Science (South China) of Ministry of Agriculture, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shuang Wang
- Key Laboratory of Animal Nutrition and Feed Science (South China) of Ministry of Agriculture, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Weiguang Xia
- Key Laboratory of Animal Nutrition and Feed Science (South China) of Ministry of Agriculture, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chuntian Zheng
- Key Laboratory of Animal Nutrition and Feed Science (South China) of Ministry of Agriculture, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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16
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Saleh M, Iraqi M, Khalil M, Camarda A. Crossbreeding analyses and polymorphic associations of gallinacin genes with growth traits in chickens. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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17
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Hosnedlova B, Vernerova K, Kizek R, Bozzi R, Kadlec J, Curn V, Kouba F, Fernandez C, Machander V, Horna H. Associations between IGF1, IGFBP2 and TGFß3 Genes Polymorphisms and Growth Performance of Broiler Chicken Lines. Animals (Basel) 2020; 10:E800. [PMID: 32380764 PMCID: PMC7277336 DOI: 10.3390/ani10050800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 01/18/2023] Open
Abstract
Marker-assisted selection based on fast and accurate molecular analysis of individual genes is considered an acceptable tool in the speed-up of the genetic improvement of production performance in chickens. The objective of this study was to detect the single nucleotide polymorphisms (SNPs) in the IGF1, IGFBP2 and TGFß3 genes, and to investigate their associations with growth performance (body weight (BW) and average daily gain (ADG) at 14, 21, 28, 35 and 42 days of age) and carcass traits in broilers. Performance (carcass) data (weight before slaughter; weights of the trunk, giblets, abdominal fat, breast muscle and thigh muscle; slaughter value and slaughter percentage), as well as blood samples for DNA extraction and SNP analysis, were obtained from 97 chickens belonging to two different lines (Hubbard F15 and Cobb E) equally divided between the two sexes. The genotypes were detected using polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) methods with specific primers and restrictase for each gene. The statistical analysis discovered significant associations (p < 0.05) between the TGFβ3 SNP and the following parameters: BW at 21, 28 and 35 days, trunk weight and slaughter value. Association analysis of BWs (at 21, 28 and 35 days) and SNPs was always significant for codominant, dominant and overdominant genetic models, showing a possible path for genomic selection in these chicken lines. Slaughter value was significant for codominant, recessive and overdominant patterns, whereas other carcass traits were not influenced by SNPs. Based on the results of this study, we suggested that the TGFβ3 gene could be used as a candidate gene marker for chicken growth traits in the Hubbard F15 and Cobb E population selection programs, whereas for carcass traits further investigation is needed.
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Affiliation(s)
- Bozena Hosnedlova
- Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic;
| | - Katerina Vernerova
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (K.V.); (V.C.)
| | - Rene Kizek
- Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic;
- Department of Human Pharmacology and Toxicology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackého 1946/1, 612 42 Brno, Czech Republic
- Department of Biomedical and Environmental Analyses, Faculty of Pharmacy with Division of Laboratory Medicine, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
| | - Riccardo Bozzi
- Food, Environment and Forestry, Animal Science Section, Department of Agriculture, University of Florence, Via delle Cascine, 5, 50144 Firenze, Italy;
| | - Jaromir Kadlec
- Department of Agricultural Products’ Quality, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic;
| | - Vladislav Curn
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic; (K.V.); (V.C.)
| | - Frantisek Kouba
- State Veterinary Administration, Regional Veterinary Administration of the South Bohemian Region, Severní 9, 370 10 České Budějovice, Czech Republic;
| | - Carlos Fernandez
- School of Pharmacy and Life Sciences, Robert Gordon University, Garthdee Road, Aberdeen AB10 7QB, UK;
| | - Vlastislav Machander
- International Testing of Poultry, Ústrašice 63, 390 02 Tábor, Czech Republic; (V.M.); (H.H.)
| | - Hana Horna
- International Testing of Poultry, Ústrašice 63, 390 02 Tábor, Czech Republic; (V.M.); (H.H.)
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18
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Ismoyowati I, Indrasanti D, Mugiyono S, Pangestu M. Phytogenic compounds do not interfere physiological parameters and growth performances on two Indonesian local breeds of ducks. Vet World 2019; 12:1689-1697. [PMID: 32009747 PMCID: PMC6925049 DOI: 10.14202/vetworld.2019.1689-1697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/18/2019] [Indexed: 11/16/2022] Open
Abstract
Aim: The present study was to investigate the interaction between duck’s breed and phytogenic compounds as feed additives in the diet on blood lipid and hematological profile, welfare, and growth performance. Materials and Methods: A total of 200 male day-old local breed ducks (Tegal and Muscovy ducks) were used in this experiment. The first factor was duck breed and the second factor was different phytogenic compounds supplementation in the diet: Garlic, turmeric, ginger, and kencur, at 3% each. The observed variables were the blood lipid profiles comprise high-density lipoprotein (HDL), low-density lipoprotein, cholesterol total, triglyceride, blood parameters, welfare (heterophil/lymphocyte [H/L] ratio), and growth performances (feed consumption, body weight gain, feed conversion ratio, and carcass percentage). Results: The interaction between breed of ducks and phytogenic compounds had a significant effect on blood triglyceride, but no significant effect on the blood lipid profile, hematological parameters, and growth performances. While, phytogenic compounds in the diet had significant effects on the blood lipid profile, heterophil (H), lymphocyte (L), and H/L ratio of ducks. The breed factors affected HDL and growth performances. Muscovy duck had a higher HDL and growth performance compare to Tegal duck. Among those, garlic most effectively reduced triglyceride level in Tegal duck. Conclusion: Phytogenic compounds 3% do not have a negative effect on the physiological parameters of ducks increase ducks welfare (H/L ratio), so it does not affect the growth performances of ducks. Muscovy duck had higher growth performances than Tegal ducks.
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Affiliation(s)
- Ismoyowati Ismoyowati
- Department of Animal Production, Faculty of Animal Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Diana Indrasanti
- Department of Animal Production, Faculty of Animal Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Sigit Mugiyono
- Department of Animal Production, Faculty of Animal Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Mulyoto Pangestu
- Department of Animal Production, Faculty of Animal Science, Jenderal Soedirman University, Purwokerto, Indonesia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia
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20
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21
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Almeida OAC, Moreira GCM, Rezende FM, Boschiero C, de Oliveira Peixoto J, Ibelli AMG, Ledur MC, de Novais FJ, Coutinho LL. Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics 2019; 20:449. [PMID: 31159736 PMCID: PMC6547531 DOI: 10.1186/s12864-019-5811-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/20/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and FST-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations. RESULTS ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. FST-based analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and FST windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine. CONCLUSIONS Identification of ROH and FST-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits.
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Affiliation(s)
| | | | | | | | | | | | | | - Francisco José de Novais
- University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo Brazil
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22
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Szalai K, Tempfli K, Lencsés-Varga E, Bali Papp Á. Genotyping of four loci in Hungarian Yellow and broiler chickens. Acta Vet Hung 2019; 67:1-10. [PMID: 30922096 DOI: 10.1556/004.2019.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Traditional selection has led to remarkable differences in allele frequencies among various chicken breeds. Indigenous and broiler-type chicken populations were genotyped for polymorphisms in thyroid hormone responsive Spot14α, prolactin (PRL), IGF-binding protein 2 (IGFBP2), and somatostatin (SST) genes in order to determine potential utilisation type-associated allele frequencies. Significant (P < 0.05) differences were detected between Hungarian Yellow and broiler populations for Spot14α, PRL, and IGFBP2 allele frequencies, whereas the same SST allele (A) was fixed in both groups. In this study, the most significant associations (P < 0.05) were found between the IGFBP2 genotypes and the measured traits (body weight, carcass weight, breast muscle weight with or without skin, breast muscle weight as a percentage of carcass weight) in the broiler population. The results can be applied for the evaluation of polymorphism effects in the analysed populations; however, contradictory allele effects in different breeds and hybrids indicate the need for cautious marker utilisation in selection programmes.
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Affiliation(s)
- Klaudia Szalai
- Széchenyi István University, Faculty of Agricultural and Food Sciences, Vár 4, H-9200 Mosonmagyaróvár, Hungary
| | - Károly Tempfli
- Széchenyi István University, Faculty of Agricultural and Food Sciences, Vár 4, H-9200 Mosonmagyaróvár, Hungary
| | - Erika Lencsés-Varga
- Széchenyi István University, Faculty of Agricultural and Food Sciences, Vár 4, H-9200 Mosonmagyaróvár, Hungary
| | - Ágnes Bali Papp
- Széchenyi István University, Faculty of Agricultural and Food Sciences, Vár 4, H-9200 Mosonmagyaróvár, Hungary
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Jawasreh K, Al Athamneh S, Al-Zghoul MB, Al Amareen A, AlSukhni I, Aad P. Evaluation of growth performance and muscle marker genes expression in four different broiler strains in Jordan. ITALIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1080/1828051x.2019.1573647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Khaleel Jawasreh
- Department of Animal Production, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
| | - Safwan Al Athamneh
- Department of Animal Production, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
| | - Mohammad Borhan Al-Zghoul
- Department of Basic Medical Veterinary Sciences, Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | | | - Ibrahem AlSukhni
- Department of Animal Production, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
| | - Pauline Aad
- Department of Sciences, FNAS Notre Dame University-Louaize, Beirut-Lebanon
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Khatri B, Hayden AM, Anthony NB, Kong BC. Whole Genome Resequencing of Arkansas Progressor and Regressor Line Chickens to Identify SNPs Associated with Tumor Regression. Genes (Basel) 2018; 9:genes9100512. [PMID: 30347774 PMCID: PMC6210987 DOI: 10.3390/genes9100512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/12/2018] [Accepted: 10/16/2018] [Indexed: 12/16/2022] Open
Abstract
Arkansas Regressor (AR) chickens, unlike Arkansas Progressor (AP) chickens, regress tumors induced by the v-src oncogene. To better understand the genetic factors responsible for this tumor regression property, whole genome resequencing was conducted using Illumina Hi-Seq 2 × 100 bp paired-end read method (San Diego, CA, USA) with AR (confirmed tumor regression property) and AP chickens. Sequence reads were aligned to the chicken reference genome (galgal5) and produced coverage of 11× and 14× in AR and AP, respectively. A total of 7.1 and 7.3 million single nucleotide polymorphisms (SNPs) were present in AR and AP genomes, respectively. Through a series of filtration processes, a total of 12,242 SNPs were identified in AR chickens that were associated with non-synonymous, frameshift, nonsense, no-start and no-stop mutations. Further filtering of SNPs based on read depth ≥ 10, SNP% ≥ 0.75, and non-synonymous mutations identified 63 reliable marker SNPs which were chosen for gene network analysis. The network analysis revealed that the candidate genes identified in AR chickens play roles in networks centered to ubiquitin C (UBC), phosphoinositide 3-kinases (PI3K), and nuclear factor kappa B (NF-kB) complexes suggesting that the tumor regression property in AR chickens might be associated with ubiquitylation, PI3K, and NF-kB signaling pathways. This study provides an insight into genetic factors that could be responsible for the tumor regression property.
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Affiliation(s)
- Bhuwan Khatri
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, NC AR 72701, USA.
| | - Ashley M Hayden
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, NC AR 72701, USA.
| | - Nicholas B Anthony
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, NC AR 72701, USA.
| | - Byungwhi C Kong
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, NC AR 72701, USA.
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Abdalla BA, Chen J, Nie Q, Zhang X. Genomic Insights Into the Multiple Factors Controlling Abdominal Fat Deposition in a Chicken Model. Front Genet 2018; 9:262. [PMID: 30073018 PMCID: PMC6060281 DOI: 10.3389/fgene.2018.00262] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/28/2018] [Indexed: 12/12/2022] Open
Abstract
Genetic selection for an increased growth rate in meat-type chickens has been accompanied by excessive fat accumulation particularly in abdominal cavity. These progressed to indirect and often unhealthy effects on meat quality properties and increased feed cost. Advances in genomics technology over recent years have led to the surprising discoveries that the genome is more complex than previously thought. Studies have identified multiple-genetic factors associated with abdominal fat deposition. Meanwhile, the obesity epidemic has focused attention on adipose tissue and the development of adipocytes. The aim of this review is to summarize the current understanding of genetic/epigenetic factors associated with abdominal fat deposition, or as it relates to the proliferation and differentiation of preadipocytes in chicken. The results discussed here have been identified by different genomic approaches, such as QTL-based studies, the candidate gene approach, epistatic interaction, copy number variation, single-nucleotide polymorphism screening, selection signature analysis, genome-wide association studies, RNA sequencing, and bisulfite sequencing. The studies mentioned in this review have described multiple-genetic factors involved in an abdominal fat deposition. Therefore, it is inevitable to further study the multiple-genetic factors in-depth to develop novel molecular markers or potential targets, which will provide promising applications for reducing abdominal fat deposition in meat-type chicken.
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Affiliation(s)
- Bahareldin A. Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Jie Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
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Rotwein P. Insulinlike Growth Factor 1 Gene Variation in Vertebrates. Endocrinology 2018; 159:2288-2305. [PMID: 29697760 PMCID: PMC6692883 DOI: 10.1210/en.2018-00259] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/19/2018] [Indexed: 12/31/2022]
Abstract
IGF1-a small, single-chain, secreted peptide in mammals-is essential for normal somatic growth and is involved in a variety of other physiological and pathophysiological processes. IGF1 expression appears to be controlled by several different signaling mechanisms in mammals, with GH playing a key role by activating an inducible transcriptional pathway via the Jak2 protein kinase and the Stat5b transcription factor. Here, to understand aspects of Igf1 gene regulation over a substantially longer timeline than is discernible in mammals, Igf1 genes have been examined in 21 different nonmammalian vertebrates representing five different classes and ranging over ∼500 million years of evolutionary history. Parts of vertebrate Igf1 genes resemble components found in mammals. Conserved exons encoding the mature IGF1 protein are detected in all 21 species studied and are separated by a large intron, as seen in mammals; the single promoter contains putative regulatory elements that are similar to those functionally mapped in human IGF1 promoter 1. In contrast, GH-activated Stat5b-binding enhancers found in mammalian IGF1 loci are completely absent, there is no homolog of promoter 2 or exon 2 in any nonmammalian vertebrate, and different types of "extra" exons not present in mammals are found in birds, reptiles, and teleosts. These data collectively define properties of Igf1 genes and IGF1 proteins that were likely present in the earliest vertebrates and support the contention that common structural and regulatory features in Igf1 genes have a long evolutionary history.
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Affiliation(s)
- Peter Rotwein
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas
- Correspondence: Peter Rotwein, MD, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, 5001 El Paso Drive, El Paso, Texas 79905. E-mail:
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Hudson NJ, Hawken RJ, Okimoto R, Sapp RL, Reverter A. Data compression can discriminate broilers by selection line, detect haplotypes, and estimate genetic potential for complex phenotypes. Poult Sci 2018. [PMID: 28633351 DOI: 10.3382/ps/pex151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accurately establishing the relationships among individuals lays the foundation for genetic analyses such as genome-wide association studies and identification of selection signatures. Of particular interest to the poultry industry are estimates of genetic merit based on molecular data. These estimates can be commercially exploited in marker-assisted breeding programs to accelerate genetic improvement. Here, we test the utility of a new method we have recently developed to estimate animal relatedness and applied it to genetic parameter estimation in commercial broilers. Our approach is based on the concept of data compression from information theory. Using the real-world compressor gzip to estimate normalized compression distance (NCD) we have built compression-based relationship matrices (CRM) for 988 chickens from 4 commercial broiler lines-2 male and 2 female lines. For all pairs of individuals, we found a strong negative relationship between the commonly used genomic relationship matrix (GRM) and NCD. This reflects the fact that "similarity" is the inverse of "distance." The CRM explained more genetic variation than the corresponding GRM in 2 of 3 phenotypes, with corresponding improvements in accuracy of genomic-enabled predictions of breeding value. A sliding-window version of the analysis highlighted haplotype regions of the genome apparently under selection in a line-specific manner. In the male lines, we retrieved high population-specific scores for IGF-1 and a cognate receptor, INSR. For the female lines, we detected an extreme score for a region containing a reproductive hormone receptor (GNRHR). We conclude that our compression-based method is a valid approach to established relationships and identify regions under selective pressure in commercial lines of broiler chickens.
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Affiliation(s)
- N J Hudson
- School of Agriculture and Food Science, University of Queensland, Gatton Campus, Queensland 4343, Australia
| | - R J Hawken
- Cobb-Vantress Inc., Siloam Springs, Arkansas 72761-1030
| | - R Okimoto
- Cobb-Vantress Inc., Siloam Springs, Arkansas 72761-1030
| | - R L Sapp
- Cobb-Vantress Inc., Siloam Springs, Arkansas 72761-1030
| | - A Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Brisbane, Queensland 4067, Australia.
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Gene Effects on Body Weight, Carcass Yield, and Meat Quality of Thai Indigenous Chicken. J Poult Sci 2018; 55:94-102. [PMID: 32055161 PMCID: PMC6756488 DOI: 10.2141/jpsa.0160159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 07/19/2017] [Indexed: 11/21/2022] Open
Abstract
The selection of rapidly growing animals in breeding programs has had inadvertent detrimental effects on meat quality. Thus, the aim of the present study was to investigate the relationship between body weight (BW) and meat quality traits, and the effects of genes encoding insulin-like growth factor I (IGF-I), insulin-like growth factor II (IGF-II), melanocortin-4 receptor (MC4R), and calpain 1 (CAPN1) on BW, carcass yield, and meat quality of the Thai indigenous chicken, Leung Hang Khao. Five hundred and ten chickens were used for genotyping. PCR-restriction fragment length polymorphism and PCR-single strand conformation polymorphism were used to determine the genotypes of IGF-I, IGF-II, MC4R, and CAPN1. BWs were collected from 0–16 weeks of age. The chickens were sacrificed at 16 weeks and individual carcass yields and meat qualities (drip loss, cooking loss, and shear force) were recorded. The correlations between BW and meat qualities were determined. Significant correlation between BW and cooking loss and shear force of breast meat and between BW and drip loss of thigh meat were detected (P<0.05); however, the magnitude of the association was low (−0.1–0.1). IGF-I was eliminated from the association analysis because genotype AA was lost and the frequency of occurrence of the AC genotype was low (0.04). Significant associations between IGF-II, CAPN1, and BW, and CAPN1 and meat quality were detected, while non-significant association between MC4R and BW was observed. The results indicated a low, negative relationship between BW and meat quality, and that the IGF-II and CAPN1 could be used as genetic markers in Leung Hang Khao chickens to improve growth and meat quality through breeding.
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Li Z, Abdalla BA, Zheng M, He X, Cai B, Han P, Ouyang H, Chen B, Nie Q, Zhang X. Systematic transcriptome-wide analysis of mRNA-miRNA interactions reveals the involvement of miR-142-5p and its target (FOXO3) in skeletal muscle growth in chickens. Mol Genet Genomics 2017; 293:69-80. [PMID: 28866851 DOI: 10.1007/s00438-017-1364-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/29/2017] [Indexed: 11/29/2022]
Abstract
The goal of this study was to perform a systematic transcriptome-wide analysis of mRNA-miRNA interactions and to identify candidates involved in the interplay between miRNAs and mRNAs that regulate chicken muscle growth. We used our previously published mRNA (GSE72424) and miRNA (GSE62971) deep sequencing data from two-tailed samples [i.e., the highest (h) and lowest (l) body weights] of Recessive White Rock (WRR) and Xinghua (XH) chickens to conduct integrative analyses of the miRNA-mRNA interactions involved in chicken skeletal muscle growth. A total of 162, 15, 173, and 27 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of the WRRh vs. XHh, WRRh vs. WRRl, WRRl vs. XHl, and XHh vs. XHl comparisons, respectively. Ingenuity Pathway Analysis revealed that gene networks identified for the WRRh vs. XHh contrast were associated with developmental disorders. Importantly, the WRRh vs. XHh contrast miRNA-mRNA network was enriched in IGF-1 signaling pathway genes, including FOXO3. A dual-luciferase reporter assay showed that FOXO3 was a target of miR-142-5p. Furthermore, miR-142-5p overexpression significantly decreased FOXO3 mRNA levels and promoted the expression of growth-related genes. These data demonstrated that miR-142-5p targets FOXO3 and promotes growth-related gene expression and regulates skeletal muscle growth in chicken. Comprehensive analysis facilitated the identification of miRNAs and target genes that might contribute to the regulation of skeletal muscle development. Our results provide new clues for understanding the molecular basis of chicken growth.
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Affiliation(s)
- Zhenhui Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Wushan Street, Tianhe District, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Bahareldin Ali Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Wushan Street, Tianhe District, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Ming Zheng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Wushan Street, Tianhe District, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Xiaomei He
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Wushan Street, Tianhe District, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Bolin Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Wushan Street, Tianhe District, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Peigong Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Wushan Street, Tianhe District, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Hongjia Ouyang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Wushan Street, Tianhe District, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Biao Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Wushan Street, Tianhe District, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Wushan Street, Tianhe District, Guangzhou, 510642, Guangdong, China. .,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China.
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Wushan Street, Tianhe District, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
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Stainton JJ, Charlesworth B, Haley CS, Kranis A, Watson K, Wiener P. Use of high-density SNP data to identify patterns of diversity and signatures of selection in broiler chickens. J Anim Breed Genet 2017; 134:87-97. [PMID: 27349343 PMCID: PMC5363361 DOI: 10.1111/jbg.12228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/24/2016] [Indexed: 12/17/2022]
Abstract
The development of broiler chickens over the last 70 years has been accompanied by large phenotypic changes, so that the resulting genomic signatures of selection should be detectable by current statistical techniques with sufficiently dense genetic markers. Using two approaches, this study analysed high-density SNP data from a broiler chicken line to detect low-diversity genomic regions characteristic of past selection. Seven regions with zero diversity were identified across the genome. Most of these were very small and did not contain many genes. In addition, fifteen regions were identified with diversity increasing asymptotically from a low level. These regions were larger and thus generally included more genes. Several candidate genes for broiler traits were found within these 'regression regions', including IGF1, GPD2 and MTNR1AI. The results suggest that the identification of zero-diversity regions is too restrictive for characterizing regions under selection, but that regions showing patterns of diversity along the chromosome that are consistent with selective sweeps contain a number of genes that are functional candidates for involvement in broiler development. Many regions identified in this study overlap or are close to regions identified in layer chicken populations, possibly due to their shared precommercialization history or to shared selection pressures between broilers and layers.
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Affiliation(s)
- J J Stainton
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - B Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - C S Haley
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.,MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - A Kranis
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.,Aviagen Ltd, Edinburgh, UK
| | | | - P Wiener
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
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31
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Fu W, Lee WR, Abasht B. Detection of genomic signatures of recent selection in commercial broiler chickens. BMC Genet 2016; 17:122. [PMID: 27565946 PMCID: PMC5002100 DOI: 10.1186/s12863-016-0430-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/22/2016] [Indexed: 02/06/2023] Open
Abstract
Background Identification of the genomic signatures of recent selection may help uncover causal polymorphisms controlling traits relevant to recent decades of selective breeding in livestock. In this study, we aimed at detecting signatures of recent selection in commercial broiler chickens using genotype information from single nucleotide polymorphisms (SNPs). A total of 565 chickens from five commercial purebred lines, including three broiler sire (male) lines and two broiler dam (female) lines, were genotyped using the 60K SNP Illumina iSelect chicken array. To detect genomic signatures of recent selection, we applied two methods based on population comparison, cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio (XP-CLR), and further analyzed the results to find genomic regions under recent selection in multiple purebred lines. Results A total of 321 candidate selection regions spanning approximately 1.45 % of the chicken genome in each line were detected by consensus of results of both XP-EHH and XP-CLR methods. To minimize false discovery due to genetic drift, only 42 of the candidate selection regions that were shared by 2 or more purebred lines were considered as high-confidence selection regions in the study. Of these 42 regions, 20 were 50 kb or less while 4 regions were larger than 0.5 Mb. In total, 91 genes could be found in the 42 regions, among which 19 regions contained only 1 or 2 genes, and 9 regions were located at gene deserts. Conclusions Our results provide a genome-wide scan of recent selection signatures in five purebred lines of commercial broiler chickens. We found several candidate genes for recent selection in multiple lines, such as SOX6 (Sex Determining Region Y-Box 6) and cTR (Thyroid hormone receptor beta). These genes may have been under recent selection due to their essential roles in growth, development and reproduction in chickens. Furthermore, our results suggest that in some candidate regions, the same or opposite alleles have been under recent selection in multiple lines. Most of the candidate genes in the selection regions are novel, and as such they should be of great interest for future research into the genetic architecture of traits relevant to modern broiler breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0430-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weixuan Fu
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA
| | | | - Behnam Abasht
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA.
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Korwin-Kossakowska A, Sartowska K, Tomczyk G, Prusak B, Sender G. Health status and potential uptake of transgenic DNA by Japanese quail fed diets containing genetically modified plant ingredients over 10 generations. Br Poult Sci 2016; 57:415-23. [PMID: 27095142 DOI: 10.1080/00071668.2016.1162281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2016] [Indexed: 10/22/2022]
Abstract
The hypothesis assumes that feed containing GMOs affects animal health and results in the transgene product accumulating in the body. Therefore, the objective of the study was to evaluate the impact of genetically modified (GM) ingredients used in poultry diets on aspects of bird health status and accumulation of transgenic DNA in eggs, breast muscle and internal organs. A total of 10 generations of Japanese quail were fed three types of diets: group A - containing GM soya (Roundup Ready) and non-GM maize, group B - containing GM maize (MON810) and non-GM soya, and group C - containing non-GM soya and maize. Bird performance traits were monitored throughout the trial. In 17-week-old animals of each generation, health examination took place on birds from each group including post-mortem necropsy and histological organ evaluation. For the purpose of transgenic DNA detection, samples of selected important tissues were taken. A molecular screening method of PCR amplification was used. The analysis of the sectional examination of birds used in the current experiment did not indicate the existence of the pathological changes caused by pathogens, nutritional factors or of environmental nature. The histopathological changes occurred in all three dietary groups and there were no statistically significant differences between the groups. There was no transgene amplification - neither CaMV35S promoter sequence nor nos terminator sequence, in the samples derived from breast muscle, selected tissues and germinal discs (eggs). According to the obtained results, it was concluded that there was no negative effect of the use of GM soya or maize with regard to bird health status or to the presence of transgenic DNA in the final consumable product.
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Affiliation(s)
- A Korwin-Kossakowska
- a Institute of Genetics and Animal Breeding , Polish Academy of Sciences , Jastrzebiec , Poland
| | - K Sartowska
- a Institute of Genetics and Animal Breeding , Polish Academy of Sciences , Jastrzebiec , Poland
| | - G Tomczyk
- b Department of Genetics Biodiversity , National Veterinary Research Institute , Pulawy , Poland
| | - B Prusak
- a Institute of Genetics and Animal Breeding , Polish Academy of Sciences , Jastrzebiec , Poland
| | - G Sender
- a Institute of Genetics and Animal Breeding , Polish Academy of Sciences , Jastrzebiec , Poland
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Anh NTL, Kunhareang S, Duangjinda M. Association of Chicken Growth Hormones and Insulin-like Growth Factor Gene Polymorphisms with Growth Performance and Carcass Traits in Thai Broilers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1686-95. [PMID: 26580435 PMCID: PMC4647076 DOI: 10.5713/ajas.15.0028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/06/2015] [Accepted: 05/19/2015] [Indexed: 11/27/2022]
Abstract
Molecular marker selection has been an acceptable tool in the acceleration of the genetic response of desired traits to improve production performance in chickens. The crossbreds from commercial parent stock (PS) broilers with four Thai synthetic breeds; Kaen Thong (KT), Khai Mook Esarn (KM), Soi Nin (SN), and Soi Pet (SP) were used to study the association among chicken growth hormones (cGH) and the insulin-like growth factor (IGF-I) genes for growth and carcass traits; for the purpose of developing a suitable terminal breeding program for Thai broilers. A total of 408 chickens of four Thai broiler lines were genotyped, using polymerase chain reaction-restriction fragment length polymorphism methods. The cGH gene was significantly associated with body weight at hatching; at 4, 6, 8, 10 weeks of age and with average daily gain (ADG); during 2 to 4, 4 to 6, 0 to 6, 0 to 8, and 0 to 10 weeks of age in PS×KM chickens. For PS×KT populations, cGH gene showed significant association with body weight at hatching, and ADG; during 8 to 10 weeks of age. The single nucleotide polymorphism variant confirmed that allele G has positive effects for body weight and ADG. Within carcass traits, cGH revealed a tentative association within the dressing percentage. For the IGF-I gene polymorphism, there were significant associations with body weight at hatching; at 2, 4, and 6 weeks of age and ADG; during 0 to 2, 4 to 6, and 0 to 6 weeks of age; in all of four Thai broiler populations. There were tentative associations of the IGF-I gene within the percentages of breast muscles and wings. Thus, cGH gene may be used as a candidate gene, to improve growth traits of Thai broilers.
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Affiliation(s)
- Nguyen Thi Lan Anh
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sajee Kunhareang
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand ; Research and Development Network Center for Animal Breeding (Native Chicken), Khon Kaen University, Khon Kaen 40002, Thailand
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand ; Research and Development Network Center for Animal Breeding (Native Chicken), Khon Kaen University, Khon Kaen 40002, Thailand
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Tempfli K, Konrád S, Kovácsné Gaál K, Pongrácz L, Bali Papp Á. Prolactin, dopamine receptor D1 and Spot14α polymorphisms affect production traits of Hungarian Yellow hens. Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Wang W, Du ZQ, Cheng B, Wang Y, Yao J, Li Y, Cao Z, Luan P, Wang N, Li H. Expression profiling of preadipocyte microRNAs by deep sequencing on chicken lines divergently selected for abdominal fatness. PLoS One 2015; 10:e0117843. [PMID: 25675096 PMCID: PMC4326283 DOI: 10.1371/journal.pone.0117843] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/01/2015] [Indexed: 12/26/2022] Open
Abstract
Through posttranscriptional gene regulation, microRNA (miRNA) is linked to a wide variety of biological processes, including adipogenesis and lipid metabolism. Although miRNAs in mammalian adipogenesis have been worked on extensively, their study in chicken adipogenesis is still very limited. To find miRNAs potentially important for chicken preadipocyte development, we compared the preadipocyte miRNA expression profiles in two broiler lines divergently selected for abdominal fat content, by sequencing two small RNA libraries constructed for primary preadipocytes isolated from abdominal adipose tissues. After bioinformatics analyses, from chicken miRNAs deposited in miRBase 20.0, we identified 225 miRNAs to be expressed in preadipocytes, 185 in the lean line and 200 in the fat line (derived from 208 and 203 miRNA precursors, respectively), which corresponds to 114 miRNA families. The let-7 family miRNAs were the most abundant. Furthermore, we validated the sequencing results of 15 known miRNAs by qRT-PCR, and confirmed that the expression levels of most miRNAs correlated well with those of Solexa sequencing. A total of 33 miRNAs was significantly differentially expressed between the two chicken lines (P<0.05). Gene ontology analysis revealed that they could target genes enriched in the regulation of gene transcription and chromatin function, response to insulin stimulation, and IGF-1 signaling pathways, which could have important roles in preadipocyte development. Therefore, a valuable information and resource of miRNAs on chicken adipogenesis were provided in this study. Future functional investigations on these miRNAs could help explore related genes and molecular networks fundamental to preadipocyte development.
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Affiliation(s)
- Weishi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Zhi-Qiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Bohan Cheng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Yuxiang Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Jing Yao
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Yumao Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Zhiping Cao
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Peng Luan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
- * E-mail: (NW); (HL)
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
- * E-mail: (NW); (HL)
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Takahashi H, Rikimaru K, Komatsu M, Uemoto Y, Suzuki K. Association between Motilin Receptor Gene Haplotypes and Growth Traits in Japanese Hinai-dori Crossbred Chickens. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:316-23. [PMID: 25049957 PMCID: PMC4093263 DOI: 10.5713/ajas.2013.13500] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/16/2013] [Accepted: 10/10/2013] [Indexed: 12/29/2022]
Abstract
We previously identified quantitative trait loci (QTL) for body weight and average daily gain in a common region between ADL0198 (chr 1: 171.7 Mb) and ABR0287 (chr 1: 173.4 Mb) on chicken chromosome 1 in an F2 resource population produced by crossing low- and high-growth lines of the Hinai-dori breed. Motilin receptor (MLNR) is a candidate gene affecting growth traits in the region. In this study, we genotyped polymorphisms of the MLNR gene and investigated its association with growth traits in a Hinai-dori F2 intercross population. All the exons of the MLNR gene in the parental population were subjected to PCR amplification, nucleotide sequenced and haplotypes identified. To distinguish resultant diplotype individuals in the F2 population, a mismatch amplification mutation assay was performed. Three haplotypes (Haplotypes 1–3) were accordingly identified. Six genotypes produced by the combination of three haplotypes (Haplotype 1, 2, and 3) were examined in order to identify associations between MLNR haplotypes and growth traits. The data showed that Haplotype 1 was superior to Haplotype 2 and 3 in body weight at 10 and 14 weeks of age, average daily gain between 4 and 10 weeks, 10 and 14 weeks, and 0 and 14 weeks of age in female in F2 females. It was concluded that MLNR is a useful marker of growth traits and could be used to develop strategies for improving growth traits in the Hinai-dori breed.
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Affiliation(s)
- Hideaki Takahashi
- Akita Prefectural Livestock Experiment Station, Daisen 019-1701, Japan
| | - Kazuhiro Rikimaru
- Akita Prefectural Livestock Experiment Station, Daisen 019-1701, Japan
| | - Megumi Komatsu
- Akita Prefectural Livestock Experiment Station, Daisen 019-1701, Japan
| | - Yoshinobu Uemoto
- National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan
| | - Keiichi Suzuki
- Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
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Wolc A, Arango J, Jankowski T, Dunn I, Settar P, Fulton JE, O'Sullivan NP, Preisinger R, Fernando RL, Garrick DJ, Dekkers JCM. Genome-wide association study for egg production and quality in layer chickens. J Anim Breed Genet 2014; 131:173-82. [PMID: 24628796 DOI: 10.1111/jbg.12086] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/14/2014] [Indexed: 12/21/2022]
Abstract
Discovery of genes with large effects on economically important traits has for many years been of interest to breeders. The development of SNP panels which cover the whole genome with high density and, more importantly, that can be genotyped on large numbers of individuals at relatively low cost, has opened new opportunities for genome-wide association studies (GWAS). The objective of this study was to find genomic regions associated with egg production and quality traits in layers using analysis methods developed for the purpose of whole genome prediction. Genotypes on over 4500 birds and phenotypes on over 13,000 hens from eight generations of a brown egg layer line were used. Birds were genotyped with a custom 42K Illumina SNP chip. Recorded traits included two egg production and 11 egg quality traits (puncture score, albumen height, yolk weight and shell colour) at early and late stages of production, as well as body weight and age at first egg. Egg weight was previously analysed by Wolc et al. (2012). The Bayesian whole genome prediction model--BayesB (Meuwissen et al. 2001) was used to locate 1 Mb regions that were most strongly associated with each trait. The posterior probability of a 1 Mb window contributing to genetic variation was used as the criterion for suggesting the presence of a quantitative trait locus (QTL) in that window. Depending upon the trait, from 1 to 7 significant (posterior probability >0.9) 1 Mb regions were found. The largest QTL, a region explaining 32% of genetic variance, was found on chr4 at 78 Mb for body weight but had pleiotropic effects on other traits. For the other traits, the largest effects were much smaller, explaining <7% of genetic variance, with regions on chromosomes 2, 12 and 17 explaining above 5% of genetic variance for albumen height, shell colour and egg production, respectively. In total, 45 of 1043 1 Mb windows were estimated to have a non-zero effect with posterior probability > 0.9 for one or more traits.
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Affiliation(s)
- A Wolc
- Department of Animal Science, Iowa State University, Ames, IA, USA; Hy-Line International, Dallas Center, IA, USA
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Jin S, Chen S, Li H, Lu Y, Xu G, Yang N. Associations of polymorphisms in GHRL, GHSR, and IGF1R genes with feed efficiency in chickens. Mol Biol Rep 2014; 41:3973-9. [PMID: 24566683 DOI: 10.1007/s11033-014-3265-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 02/12/2014] [Indexed: 01/03/2023]
Abstract
The ghrelin (GHRL), ghrelin receptor (GHSR), and insulin-like growth factor 1 receptor (IGF1R) genes have crucial effects on body weight (BW), body weight gain (BWG), feed intake (FI), and feed conversion ratio (FCR) in many species. However, few studies on associations of GHRL, GHSR, and IGF1R with BWG, FI, and FCR have been reported in chickens. In this study, 16 SNPs in GHRL, GHSR, and IGF1R genes were genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The objective of this study was to examine the associations of GHRL, GHSR, and IGF1R genes polymorphisms with BW at 49 days (BW49) and 70 days (BW70) of age, BWG, FI, and FCR in the interval in two yellow meat-type populations with a total of 724 birds. The results showed that rs15675067 of GHRL was significantly associated with BW70, BWG, and FCR (P < 0.05). For GHSR, rs16675844 had significant effects on FI and FCR (P < 0.01), and that rs14678932 showed significant association with BWG and FI (P < 0.05). Rs14011780 of IGF1R was strongly associated with BW49, BW70, and FCR (P < 0.05). Furthermore, haplotypes based on three SNPs of rs14986828, rs15675067, and rs15675065 in GHRL were significantly associated with BW70 and FCR (P < 0.05). Meanwhile, a three-SNP haplotype comprising rs14011783, rs14011780, and rs14011776 in IGF1R showed significant effects on BW49, BW70, and FCR (P < 0.05). Therefore, it was concluded that the identified SNPs and analyzed haplotypes in this study might be useful for broiler breeding programs.
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Affiliation(s)
- Sihua Jin
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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Pandey N, Singh R, Saxena V, Shit N, Singh R, Sharma R, Sastry K. Effect of IGF1 gene polymorphism and expression levels on growth factors in Indian colored broilers. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Boschiero C, Jorge EC, Ninov K, Nones K, do Rosário MF, Coutinho LL, Ledur MC, Burt DW, Moura ASAMT. Association of IGF1 and KDM5A polymorphisms with performance, fatness and carcass traits in chickens. J Appl Genet 2012; 54:103-12. [DOI: 10.1007/s13353-012-0129-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/26/2012] [Accepted: 12/06/2012] [Indexed: 12/13/2022]
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Qanbari S, Strom TM, Haberer G, Weigend S, Gheyas AA, Turner F, Burt DW, Preisinger R, Gianola D, Simianer H. A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens. PLoS One 2012; 7:e49525. [PMID: 23209582 PMCID: PMC3510216 DOI: 10.1371/journal.pone.0049525] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 10/10/2012] [Indexed: 12/12/2022] Open
Abstract
In most studies aimed at localizing footprints of past selection, outliers at tails of the empirical distribution of a given test statistic are assumed to reflect locus-specific selective forces. Significance cutoffs are subjectively determined, rather than being related to a clear set of hypotheses. Here, we define an empirical p-value for the summary statistic by means of a permutation method that uses the observed SNP structure in the real data. To illustrate the methodology, we applied our approach to a panel of 2.9 million autosomal SNPs identified from re-sequencing a pool of 15 individuals from a brown egg layer line. We scanned the genome for local reductions in heterozygosity, suggestive of selective sweeps. We also employed a modified sliding window approach that accounts for gaps in the sequence and increases scanning resolution by moving the overlapping windows by steps of one SNP only, and suggest to call this a “creeping window” strategy. The approach confirmed selective sweeps in the region of previously described candidate genes, i.e. TSHR, PRL, PRLHR, INSR, LEPR, IGF1, and NRAMP1 when used as positive controls. The genome scan revealed 82 distinct regions with strong evidence of selection (genome-wide p-value<0.001), including genes known to be associated with eggshell structure and immune system such as CALB1 and GAL cluster, respectively. A substantial proportion of signals was found in poor gene content regions including the most extreme signal on chromosome 1. The observation of multiple signals in a highly selected layer line of chicken is consistent with the hypothesis that egg production is a complex trait controlled by many genes.
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Affiliation(s)
- Saber Qanbari
- Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August University, Göttingen, Germany.
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Sparkman AM, Schwartz TS, Madden JA, Boyken SE, Ford NB, Serb JM, Bronikowski AM. Rates of molecular evolution vary in vertebrates for insulin-like growth factor-1 (IGF-1), a pleiotropic locus that regulates life history traits. Gen Comp Endocrinol 2012; 178:164-73. [PMID: 22569170 DOI: 10.1016/j.ygcen.2012.04.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 03/24/2012] [Accepted: 04/23/2012] [Indexed: 11/20/2022]
Abstract
Insulin-like growth factor-1 (IGF-1) is a member of the vertebrate insulin/insulin-like growth factor/relaxin gene family necessary for growth, reproduction, and survival at both the cellular and organismal level. Its sequence, protein structure, and function have been characterized in mammals, birds, and fish; however, a notable gap in our current knowledge of the function of IGF-1 and its molecular evolution is information in ectothermic reptiles. To address this disparity, we sequenced the coding region of IGF-1 in 11 reptile species-one crocodilian, three turtles, three lizards, and four snakes. Complete sequencing of the full mRNA transcript of a snake revealed the Ea-isoform, the predominant isoform of IGF-1 also reported in other vertebrate groups. A gene tree of the IGF-1 protein-coding region that incorporated sequences from diverse vertebrate groups showed similarity to the species phylogeny, with the exception of the placement of Testudines as sister group to Aves, due to their high nucleotide sequence similarity. In contrast, long-branch lengths indicate more rapid divergence in IGF-1 among lizards and snakes. Additionally, lepidosaurs (i.e., lizards and snakes) had higher rates of non-synonymous:synonymous substitutions (dN/dS) relative to archosaurs (i.e., birds and crocodilians) and turtles. Tests for positive selection on specific codons within branches and evaluation of the changes in the amino acid properties, suggested positive selection in lepidosaurs on the C domain of IGF-1, which is involved in binding affinity to the IGF-1 receptor. Predicted structural changes suggest that major alterations in protein structure and function may have occurred in reptiles. These data propose new insights into the molecular co-evolution of IGF-1 and its receptors, and ultimately the evolution of IGF-1's role in regulating life-history traits across vertebrates.
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Affiliation(s)
- Amanda M Sparkman
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA 50011, USA
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43
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Zhang H, Hu X, Wang Z, Zhang Y, Wang S, Wang N, Ma L, Leng L, Wang S, Wang Q, Wang Y, Tang Z, Li N, Da Y, Li H. Selection signature analysis implicates the PC1/PCSK1 region for chicken abdominal fat content. PLoS One 2012; 7:e40736. [PMID: 22792402 PMCID: PMC3394724 DOI: 10.1371/journal.pone.0040736] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 06/12/2012] [Indexed: 12/18/2022] Open
Abstract
We conducted a selection signature analysis using the chicken 60k SNP chip in two chicken lines that had been divergently selected for abdominal fat content (AFC) for 11 generations. The selection signature analysis used multiple signals of selection, including long-range allele frequency differences between the lean and fat lines, long-range heterozygosity changes, linkage disequilibrium, haplotype frequencies, and extended haplotype homozygosity. Multiple signals of selection identified ten signatures on chromosomes 1, 2, 4, 5, 11, 15, 20, 26 and Z. The 0.73 Mb PC1/PCSK1 region of the Z chromosome at 55.43-56.16 Mb was the most heavily selected region. This region had 26 SNP markers and seven genes, Mar-03, SLC12A2, FBN2, ERAP1, CAST, PC1/PCSK1 and ELL2, where PC1/PCSK1 are the chicken/human names for the same gene. The lean and fat lines had two main haplotypes with completely opposite SNP alleles for the 26 SNP markers and were virtually line-specific, and had a recombinant haplotype with nearly equal frequency (0.193 and 0.196) in both lines. Other haplotypes in this region had negligible frequencies. Nine other regions with selection signatures were PAH-IGF1, TRPC4, GJD4-CCNY, NDST4, NOVA1, GALNT9, the ESRP2-GALR1 region with five genes, the SYCP2-CADH4 with six genes, and the TULP1-KIF21B with 14 genes. Genome-wide association analysis showed that nearly all regions with evidence of selection signature had SNP effects with genome-wide significance (P<10(-6)) on abdominal fat weight and percentage. The results of this study provide specific gene targets for the control of chicken AFC and a potential model of AFC in human obesity.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, People's Republic of China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Xiaoxiang Hu
- College of Biological Science, China Agricultural University, Beijing, People's Republic of China
| | - Zhipeng Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, People's Republic of China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Yuandan Zhang
- Animal Genetics and Breeding Unit, University of New England, Armidale, New South Wales, Australia
| | - Shouzhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, People's Republic of China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, People's Republic of China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Li Ma
- Department of Animal Science, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Li Leng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, People's Republic of China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Shengwen Wang
- Department of Animal Science, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Qigui Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, People's Republic of China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Yuxiang Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, People's Republic of China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Zhiquan Tang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, People's Republic of China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Ning Li
- College of Biological Science, China Agricultural University, Beijing, People's Republic of China
| | - Yang Da
- Department of Animal Science, University of Minnesota, Saint Paul, Minnesota, United States of America
- * E-mail: (HL); (YD)
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, People's Republic of China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
- * E-mail: (HL); (YD)
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Signatures of selection in the genomes of commercial and non-commercial chicken breeds. PLoS One 2012; 7:e32720. [PMID: 22384281 PMCID: PMC3287981 DOI: 10.1371/journal.pone.0032720] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 02/03/2012] [Indexed: 12/20/2022] Open
Abstract
Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations.
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45
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Mitchell A, Rosebrough R, Taicher G, Kovner I. In vivo measurement of body composition of chickens using quantitative magnetic resonance. Poult Sci 2011; 90:1712-9. [DOI: 10.3382/ps.2010-01156] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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46
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Sato S, Ohtake T, Uemoto Y, Okumura Y, Kobayashi E. Polymorphism of insulin-like growth factor 1 gene is associated with breast muscle yields in chickens. Anim Sci J 2011; 83:1-6. [PMID: 22250732 DOI: 10.1111/j.1740-0929.2011.00917.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Insulin-like growth factor-1 (IGF1) plays an important role in muscle development in chickens. In this study, an F2 chicken population of 362 individuals, obtained from an intercross between high breast muscle yield line males and low breast muscle yield (LB) line females, was constructed for investigating the associations between IGF1 gene and breast muscle yields. The IGF1 sequence was investigated in the grandparents. There were no differences in the exon sequences. However, sequence analysis of the IGF1 promoter revealed a known single nucleotide polymorphism (g.570C>A) in LB line grandparents. PCR - restriction fragment length polymorphism was used for screening the F2 population, which was evaluated for body weight (BW), carcass weight (CW), breast muscle weight (BMW), and breast fillet weight (BFW). Significant associations with the polymorphism were detected for BMW, BFW, BMW% and BFW%, although there were no associations between the polymorphism and BW or CW. The allelic effect on BMW, BFW, BMW% and BFW% acted in additive and dominance modes. We confirmed that the g.570C>A polymorphism is significantly associated with breast muscle yields in the F2 population. Therefore, this polymorphism in the IGF1 gene may help improve breast muscle yields by marker-assisted selection.
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Affiliation(s)
- Shinichi Sato
- National Livestock Breeding Center, Nishigo, Fukushima, Japan.
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47
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Luna-Nevarez P, Rincon G, Medrano JF, Riley DG, Chase CC, Coleman SW, VanLeeuwen DM, DeAtley KL, Islas-Trejo A, Silver GA, Thomas MG. Single nucleotide polymorphisms in the growth hormone–insulin-like growth factor axis in straightbred and crossbred Angus, Brahman, and Romosinuano heifers: Population genetic analyses and association of genotypes with reproductive phenotypes1. J Anim Sci 2011; 89:926-34. [DOI: 10.2527/jas.2010-3483] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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48
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Insulin-like growth factor-I gene polymorphism and its association with growth and slaughter characteristics in broiler chickens. ACTA ACUST UNITED AC 2011. [DOI: 10.2478/v10146-011-0017-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Insulin-like growth factor-I gene polymorphism and its association with growth and slaughter characteristics in broiler chickensChicken insulin-like factor 1 gene (IGF1) is a biological candidate gene for the investigation of growth, body composition, and metabolic and skeletal traits, and is also a positional candidate gene for growth and fat deposition in chickens. Two broiler populations Ross 308 and Cobb 500 were used to study the relationship between IGF1 gene polymorphism and phenotypic traits. A single nucleotide polymorphism (SNP) was identified in 132 individuals using the PCR-RFLP technique. Genotypical frequencies were, for genotype AA: 0.83-0.86, and for AC: 0.14-0.17. Associations between IGF1 promotor polymorphism and liver weight (P≤0.05) and liver weight as a percentage of the weight of the poultry carcass with the giblets (P≤0.05), were found in the AC genotype in a comparison of broiler homozygous chickens AA in the Cobb 500 line. In these broilers, the breast muscle and leg muscle weight in the AC genotype were higher, and abdominal fat weight lower compared with AA genotype chickens, but these differences were not significant.
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49
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Seyedabadi HR, Amirinia C, Amirmozafari N, Torshizi RV, Chamani M, Aliabad AJ. Association of apolipoprotein B gene with body growth and fatness traits in Iranian commercial broiler lines. Livest Sci 2010. [DOI: 10.1016/j.livsci.2010.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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50
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Tang S, Sun D, Ou J, Zhang Y, Xu G, Zhang Y. Evaluation of the IGFs (IGF1 and IGF2) genes as candidates for growth, body measurement, carcass, and reproduction traits in Beijing You and Silkie chickens. Anim Biotechnol 2010; 21:104-13. [PMID: 20379887 DOI: 10.1080/10495390903328090] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Insulin-like growth factors are crucial in cellular growth, differentiation, and reproduction by mediating many of the actions of growth hormone in chickens. To determine whether insulin-like growth factors genes (IGFs) are associated with important economic traits in chicken or not, we herein analyzed the association between two single nucleotide polymorphisms (SNPs) within IGF1 and IGF2 and twenty-seven growth, body measurement, carcass, and reproduction traits in two Chinese native breeds, i.e., Beijing You and Silkies. With marker-trait association analysis, we found that SNP IGF1-PstI, within the 5' flanking region of IGF1, was significantly associated with body weight at 8 (BW8), 10 (BW10), and 13 (BW13) wk of age; and shank length (SL13) and shank circumference (SC13) at 13 wk of age in Silkie population (P < 0.05). The SNP IGF2-MspI within the exon2 of IGF2 showed a significant association with body weight (BW17) and carcass weight (CW17) at 17 wk of age in Beijing You population (P < 0.05). Our findings implied that the SNPs within IGF1 and IGF2 genes could be in linkage disequilibrium with the actual causative mutations that affect growth and carcass traits.
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Affiliation(s)
- Shaoqing Tang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, China Agricultural University, Beijing, China
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